from Bio.PDB import PDBParser
from biodata import file_dict
import ezb
structure_files = file_dict('structures with 1qd5', ['aligned_(.*).pdb'])
parser = PDBParser()
with warnings.catch_warnings():
warnings.simplefilter('ignore')
structures = [(name, parser.get_structure(name, path)) \
for name, path in structure_files.items()]
structures = CIDict(structures)
with open('cored 1 selections with 1qd5.csv', 'rb') as f:
reader = csv.reader(f)
inclusive_selections = ezb.selections_by_resi(reader)
with open('beta_selections.csv', 'rb') as f:
reader = csv.reader(f)
beta_selections = ezb.selections_by_resi(reader)
exclusive_selections = CIDict()
for name, selection in beta_selections.items():
exclusive_selections.update(((name, list(set(selection).intersection(
set(inclusive_selections[name])))),))
with open('cored 1 centers with 1qd5.csv', 'rb') as f:
reader = csv.reader(f)
inc_centers = ezb.load_centers(reader)
# Daniel's aligned pdb files are missing b factors, and perhaps
# some other information, which causes Biopython to give hundreds
# or thousands of warnings when loading them. The following code
# suppresses warnings
with warnings.catch_warnings():
warnings.simplefilter('ignore')
structures = [(name, parser.get_structure(name, path)) \
for name, path in structure_files.items()]
structures = CIDict(structures)
# Load the selections that should have been used
with open('exc centers/exc selections.csv', 'rb') as f:
reader = csv.reader(f)
beta_selections = ezb.selections_by_resi(reader)
right_selections = CIDict()
for name, selection in beta_selections.items():
right_selections.update(((name, selection),))
with open('exc centers.csv', 'rb') as f:
exc_centers = ezb.load_centers(csv.reader(f))
def moments(path, selections, centers):
with open('published params.csv', 'rb') as f:
reader = csv.reader(f)
new_calc = ezb.Calculator(reader, normalize = True)
moments = CIDict()